Kindred Spirits
by SGAFan
Summary: Major Sheppard and Dr. McKay exploring Atlantis. Sounds innocent enough. But when things go a little awry, both men make some unexpected realizations. Early Season 1 story


**Kindred Spirits  
**

**Just a little warning, there is mild language in this story…nothing too heavy!**

"You know, we could've just transported here."

John Sheppard paused mid-stride, lowered his P-90 and glanced sideways at McKay. "We're _exploring_ the city, Rodney." He pointed his gun down an intersecting hallway; it's light bouncing off the walls, before continuing on. "That takes all the fun out of it."

"Fun," McKay snorted, looking around. "Fun is…hmm, interesting."

"That's helpful," Sheppard glanced sideways at McKay, earning himself an annoyed look.

"I meant the LSD reading. It's weird."

Sheppard paused, his brow crinkling. "LSD? Somehow I don't think you're talking about acid."

"Life…signs…detector," McKay spelled out, his tone annoyed.

"I can't believe Ford's name stuck," Sheppard muttered as he stepped backwards and stopped next to McKay. He looked down at the LSD. "Define weird."

"Strange, unusual…weird. Haven't we gone through this before? I can't read anything beyond that door." He pointed ahead.

Sheppard's gaze followed Rodney's gesture, his eyes settling on a sealed doorway about twenty feet away. "Let's check it out." He walked forward a few steps and stopped, a sigh from behind grabbing his attention.

"You know, we always get in trouble when you say that."

Giving McKay his best no nonsense look, John continued towards the door, smiling slightly at the heavy footsteps following him. "You know you can't resist, Rodney." He quirked a brow at the non-committal grunt McKay gave him. Reaching up, John lightly tapped the center crystal next to the door, his smile fading as nothing happened. After a moment, he pressed it again, this time a little harder. Once again, the door didn't respond.

"Of course," McKay muttered as he stepped around Sheppard and pushed the Major's arm out of his way. "Let's check it out," he mimicked Sheppard sarcastically, "translation: Rodney, we're going to go look at something and we have no idea what we're doing, so, it's up to you to figure it out."

Sheppard shook his head at McKay and stepped away. "That's why you're indispensable, Rodney."

"Damn right," McKay muttered as he pulled the cover off the door controls. He quickly shifted the top two crystals around and looked up as the door groaned for a moment before popping open.

Sheppard lifted his P-90 and shined the light through the doorway. Beyond the threshold, it was pitch black, the only light being a narrow stream coming from the Major's flashlight. He lowered his gun and tapped the call button on his radio twice. "Control, this is Sheppard. We've found an unusual room on the west pier of the city. We're checking it out now, will advise once we know something."

"We read you, Major, be careful." The concerned voice of Dr. Elizabeth Weir answered him.

"Copy that, control. Sheppard out." Lifting his gun, the Major slowly walked forward, McKay right beside him.

As they stepped through the doorway, a small light overhead hummed to life, its dim glow revealing the shadow of a narrow countertop winding through the center of the room; a small island in an otherwise bare room.

McKay stepped around Sheppard and approached the island. He scanned his light across its surface, a quiet "ah" escaping him as he located the computer console.

Sheppard came up behind him. "What is this place? Another research lab?"

"I'm not sure. The layout is different than the ones we've encountered before." McKay tapped several different controls, frowning as they refused to function. "Huh, weird."

"You really need to find another word to describe things, Rodney," Sheppard quipped as he watched the scientist kneel and shine his light under the panel.

McKay paused and glanced up at the Major. "How about strange?" He asked sarcastically before he once again returned his attention to the underside of the console.

"Twilight Zone strange or snow in Baton Rouge strange?" Sheppard stared evenly at McKay as the scientist once again looked up at him.

"What is with you and the metaphors?" He waved his hand before the Major could answer. "Never mind. Let me spell it out for you: This…panel…has…no…power." He enunciated each word before once more disappearing under the console.

Bemused, Sheppard shook his head. "Thank you." A mischievous smile crept onto his face. "That's weird." His smile widened as a sigh of near martyred proportions came from under the panel.

"Why me?"

Sheppard's retort died on his lips as a loud grinding sound came from the doorway. Reflexively he raised his gun his eyes scanning for danger and watched as, with a resounding boom, the door slammed shut. He stepped sideways as McKay scrambled out from under the console.

"What was that?" He pointed his flashlight up, scanning the low ceiling before looking towards the Major.

Sheppard cocked his head towards the door. "That."

"Oh no," Rodney groaned as he quickly stepped around the island and approached the doorway. Hastily, he shined his flashlight all around the doorframe. "There are no controls. How do we open it?"

Sheppard raised his brows. "You're asking me?"

"I was speaking metaphorically." McKay continued to scan the door jam.

"Now who's got a thing for metaphors?" Sheppard teased. His eyes narrowed, all humor leaving them as McKay abruptly turned to face him. There was a new tension to Rodney's otherwise neutral expression.

"We can decide who has the rights to metaphors later." McKay's voice rose slightly in agitation, "right now I need to get this door open."

"Easy, Rodney, you'll figure it out," Sheppard replied quietly.

"Oh sure!" McKay's voice grew louder. "Because that's how things work! Let's see what trouble we can get into, so Rodney can get us out!"

"McKay!" Sheppard matched the scientist's volume, silencing him. He once more lowered his voice. "Calm down."

Rodney's shoulders sagged. "I just have a problem with…confined spaces."

The Major nodded and looked around. "It's really not that small, Rodney." He shined his light on the far wall. "That has to be at least twenty feet away. Don't think of it as a small room…just a really big closet."

McKay rounded the island and once more knelt under the console. He propped his flashlight up against the edge of the counter, directing its beam at the control circuits and freeing his hands for work. "That doesn't help, Major."

Sheppard shrugged. "Sorry." He clicked his radio twice before speaking. "Control, this is Sheppard. We've run into a bit of…ah…trouble here." His frown deepened at the silence that met his transmission. He clicked his radio again. "Control, do you copy?" Silence once more greeted his words.

"Terrific," McKay muttered.

"That's…strange," Sheppard lifted his gun, shined the light around the room, and took a few steps away from McKay. "I'm going to check out the rest of the room and see if there is anything useful."

Briefly, Rodney peeked out from under the console. "I wish you'd stop saying that."

Never breaking stride, Sheppard smiled as he slowly crossed the room, flashing his light this way and that. "You know, for a research lab, this place is pretty empty."

"Well," Rodney grunted and shifted his weight, scooting himself further under the console, "we don't really know what this room was used for."

Sheppard nodded to himself as he moved along the back wall. "There isn't anything here." He turned, shining his light on McKay's legs sticking out from under the console. "You going to be able to get that door open?"

"Only if you stop interrupting me." Rodney peeked out from under the counter and flashed the Major a cold look.

"Right." John's brows quirked as he leaned back against the wall. Lowering his P-90 he crossed his arms and propped one foot against the wall behind him. "Pretend I'm not here."

"Already doing that," McKay's distracted voice answered.

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"Damn it!"

Sheppard opened his eyes and squinted at McKay. He flipped on the light on his gun. "You're sure I can't help you?"

"No, Major, you can't." McKay slid out from under the console and stood, stretching.

"I could…"

"Major," McKay interrupted in irritation, "instead of standing here explaining what you could do, it's faster for me to do it myself!"

Sheppard shifted his weight and crossed his legs in front of him. Sometime in the last few hours, he'd sat down, resigning himself to waiting as McKay tried to solve their technical problems. "Well, you don't have to be so snippy about it."

"I've been at this for two hours with no results! Don't expect me to be cheerful." McKay shot back.

"You're never nice anyway," Sheppard retorted. He cocked his head. "Why is that?"

"What?" McKay, exasperated, turned away from the console and fixed Sheppard with an annoyed glare.

Sheppard shrugged. "Well, don't take this personally, Rodney, but you're really an ass most of the time." He watched carefully as the annoyance on McKay's face melted away and was replaced by what John could only call a practiced neutral expression.

"Yep." McKay turned back to the console and pushed a button experimentally, sighing as nothing happened. He once more disappeared under the counter.

John shook his head and stood up. Slowly, he walked over to McKay's position and knelt. He watched as the doctor's hand felt around on the floor, searching for a tool. John picked up a small screwdriver and handed it under the console to Rodney. "So?" He prodded, "why?"

Rodney paused for a moment and looked up at him. "Why what?"

Sheppard chuckled. "Why do you work so hard to be such an ass, Rodney?"

McKay stared at him for a long moment before returning his attention to the circuits above his head. "Major, I'm trying to get us out of here. It's hardly the time to talk about this."

John shifted his weight and sat down, leaning against a leg of the counter. "Well, you're a pretty smart guy…" he smiled as Rodney grunted at his statement, "you'd just get along better with people if you tried to be a little nicer, that's all."

"So now you're a psychiatrist, Major? What other talents do you have?"

Sheppard's gaze narrowed. While decidedly sarcastic, McKay's voice had a hint of defensiveness. He'd touched a nerve in the doctor. "I'm just sayin'…"

"It's self defense," McKay interrupted quietly.

Sheppard glanced over at McKay's legs. He leaned forward and looked under the console, making eye contact with the doctor. "Come again?"

Rodney shook his head and resumed fiddling with the circuits. "Major, do you know how people like me get treated? I can think circles around 99 percent of the people I've ever met. Do you know how people react to that? The looks you get? The whispered comments by people when they think you can't hear them?" Rodney tested another circuit and jumped as an electric shock shot through his hand. "Ow!"

"McKay? Sheppard instantly pulled his legs under himself and into a squatting position, "you okay?"

Rodney shook his hand a couple times and nodded. "Yeah. At least we know there's some power here…"

John tapped Rodney's foot a couple times. "Come out from under there, McKay and take a rest before you hurt yourself."

"Major…"

Sheppard leaned over, once more making eye contact with Rodney. "Now, Rodney." He cracked a small smile as the doctor sighed once and scooted out from under the console. Rodney slid sideways before leaning back on a leg of the counter.

Sheppard sat back down again a few feet away from the doctor. He reached into his vest pocket and pulled out two Power Bars, tossing one to McKay. "Here."

Rodney looked down as the Power Bar landed in his lap. "Oh, thanks." He pulled the wrapper off and took a big bite.

"So," Sheppard swallowed a bite of his bar, "you got tired of people treating you like a freak, so you decided to be mean first?"

"It works," McKay mumbled around his chewing.

"Well, yeah," John shrugged, "but you don't let anyone be nice either."

Rodney's shoulders sagged. "Major, as long as I can remember, I've always wanted to know how things worked. Drove my parents crazy. I remember one time…" He glanced at Sheppard. "Well, never mind. But when I was 12 I wanted to play piano. I wanted to be a concert pianist. I worked hard at it, but one day my instructor told me to stop playing. She said I was technically good, but not musically. I didn't have the musical talent." McKay paused and looked down, his hands absently wrinkling the wrapper to his Power Bar.

"I turned back to science, because I was good at it. But it's a double-edged sword. The better I got at science…" He shrugged, and took another bite of his bar.

Sheppard glanced over at Rodney, watching as he slowly chewed and swallowed his bite before crumpling up the wrapper and slipping it into a pocket of his vest. McKay looked over at him, some of the neutrality of his expression giving way to hints of vulnerability.

"Kids can really be mean to each other, Major." Rodney looked away, his gaze fixing on the far wall. "When I was a junior in high school I showed up a guy in my chemistry class by pointing out what he was doing wrong and giving him the correct answer, in front of everyone. That got me a black eye."

Sheppard winced. "Ouch."

"Yeah," McKay cracked a half smile and looked down at his fidgeting hands. "Not sure why I just told you that." His voice was slightly self-conscious.

John stared for a long moment at Rodney before finishing his own snack. "Me either," he answered. Sheppard glanced at the doctor and smiled, satisfied when McKay smiled and chuckled back.

Sheppard wadded up the wrapper for his bar and stretched his legs out. "Well, at least you didn't show up your teachers."

"Oh yeah," McKay immediately responded, "been there, done that…" his sentence trailed off as he fixed the Major with a searching gaze. "You too?" His voice held a note of surprise.

Sheppard chuckled. "Yep. Didn't expect that from a military man?"

"It's not that…" McKay stammered, "Okay, it is that. I just have a hard time…never mind. You were saying?"

"Trigonometry."

"What?" McKay's voice was confused. "What about it?"

"Well," Sheppard settled back and crossed his arms across his chest, "math was always easy for me. But once, when I was in the 10th grade, I popped off an answer to a complex equation involving imaginary numbers." John grinned. "Mr. Harrison stood there, slack jawed and stared at me." His smile faded and it was his turn to fidget. "So did everyone else in the class. After working the equation out on the chalkboard, Mr. Harrison saw that I was right, but that really didn't matter. The looks from the other kids in the class…well," he shrugged, "I've never been more insecure in my life." Sheppard lowered his head, a thoughtful expression settling onto his face. After a moment, he glanced over at McKay. "Did you know I played football?"

McKay snorted. "Football. Of course you did."

"You're being an ass again, Rodney," Sheppard replied quietly.

Rodney sighed. "You were saying?"

"I was a quarterback." One side of his mouth turned up in a lopsided smile. "I was good. All state my senior year. Coach wanted me to go on a play college ball, but my dad…" John quirked his eyebrows, "well, when your father is Colonel Marcus Sheppard, personally decorated by the President…" his voice trailed off into a chuckle. "I went to the Air Force Academy instead."

"You didn't want to be a pilot?" McKay stared at Sheppard incredulously.

"Hell yes," Sheppard immediately responded. "Bein' a soldier's in my blood, Rodney. Besides, where else could I get paid to fly the best machines in the world?" Sheppard waved absently, his smile fading, "anyway, a locker room full of football players who find out you're good at math isn't a cakewalk either, so…" he shrugged, "I stopped."

"Stopped? Stopped what?" Rodney questioned. "Doing math?"

John shrugged. "No, just stopped being obvious about it." Sheppard stared long at McKay, his expression thoughtful, before looking away and chuckling.

"What is it now?" Rodney glared in annoyance at the Major, his irritated look deepening as Sheppard's smile widened. "Sure, let's all laugh at the scientist."

"I'm not laughing at you, Rodney," Sheppard waved his hand absently.

"Then what's so funny?" McKay asked in exasperation.

"The whole irony of this." John arched his eyebrows. "Don't you see it?"

"No, Major, I don't," Rodney's voice was heavy with sarcasm. "Why don't you enlighten me?"

Sheppard fixed McKay with a thoughtful look. "I'm the soldier, you're the civilian, yet in some ways you've got more guts than I do."

Rodney's eyes narrowed in confusion. "What?"

"I took the easy way out, Rodney," Sheppard explained. "Instead of just being who I am, I hid it. You, on the other hand, refused to hide who you were just for the sake of being comfortable around other people." He smiled, his expression turning mischievous. "You're an acerbic, asshole, Rodney, but at least you don't try and hide who you are."

McKay wrinkled his brows, his eyes flicking around the room as he considered Sheppard's words. "I'm not sure if I should thank you, or tell you to piss off," he muttered.

John chuckled. "It's meant as a compliment…sort of…"

McKay chuckled at the infectious nature of Sheppard's tone. "Right…a compliment." He shook his head, his smile fading. "Well, as long as we're bearing our souls here…you don't think this is foretelling certain doom, do you?" His voice took on a slightly panicked tone.

Sheppard rolled his eyes. "Relax, Rodney. By now, Elizabeth has tried to contact us and got nothing but silence. I'm sure she's sent teams out to find us. She knows we're in the west pier. The search teams will see the open door control panel and know we're in here. It's just a matter of time before they find us."

"Okay," McKay conceded. "Because I don't want to jinx our fate by saying anything…"

"Rodney," Sheppard interrupted. "You were saying something about bearing souls? Because I'm not going to let you off without telling me what you were going to tell me. You're not leaving here with that kind of leverage." He grinned at the Doctor.

Rodney chuckled. "It's not as ironic as you think, Major," his smile faded. "You know? I hate crowds of people…I hate just being around a few people. Give me a computer or a Zed-PM or something…not alive, and I'm happy, but people?" he sighed. "You have the guts to continue to talk…" Rodney absently waved his hands as he struggled to find the right words, "…to interact with people. Me? I pushed…everyone away."

Sheppard's gaze narrowed. Something about what McKay said caught his attention. "Everyone…or someone?"

Rodney's gaze turned distant. "Both."

"Somehow I don't think we're speaking in general terms here, McKay. Who, exactly, are you talking about?" John questioned.

"People in general…Monica in particular."

"Monica?" Sheppard's brows arched.

"When I was 24." Rodney continued, his expression distant as he recalled memories, "I was finishing up my Masters in Astrophysics when I met her."

Sheppard nodded and waited patiently through a prolonged silence. After a minute passed, he glanced at McKay. "And?"

"And I just ended up pushing her away, just like everyone else. A small smile formed on Rodney's face. "Not a day goes by that I don't think about her, in some small way." McKay blinked and took a deep breath. "I should've been married with…" he shrugged, "I don't know…three kids by now?" The distant and vulnerable expression on his face disappeared behind the practiced, stern expression Rodney usually wore.

Sheppard smiled. "Then you probably wouldn't have come on this fun adventure, McKay."

Rodney snorted. "Oh yeah, life sucking Wraith. Sounds fun to me." He laughed quietly, tension leaving him.

John chuckled with him, both men letting their unexpected conversation slip away. After a few minutes, Sheppard's laughing subsided and he took a deep breath. "Look, Rodney, we all make mistakes. We just got to, kind of learn to live with them."

McKay flashed Sheppard the briefest of understanding looks before his acerbic attitude took over. "Oh, thank you Dr. Freud." Scooting across the floor, Rodney once more disappeared under the computer console.

Sheppard chuckled quietly before standing and stretching his legs. He strolled casually around the room, keeping quiet and letting McKay do his work. He shook his head as his thoughts turned to the Canadian doctor. At first, he'd read Rodney as just a jerk, highly intelligent, but a jerk. But the more he had worked with McKay, the more he'd begun to doubt that assessment…and that alone bothered him. For as long as he could remember, he'd always been a pretty fast and accurate judge of people, but as he'd worked more and more with Rodney and in the light of what he'd just learned, Sheppard had to consider that maybe he'd completely misread the acerbic doctor.

John turned his head, a tapping sound pulling him from his thoughts. As quickly as he noticed it, the tapping stopped. "McKay? Did you hear that?"

"Hear what?" Rodney's muffled voice was annoyed. "Major I can't get anything done if you keep bugging me!"

Sheppard ignored Rodney's comments and walked towards the door. Once again, a quiet tapping could be heard. He stopped in front of the door and listened, a smile popping to his face as he realized the sound was coming from the other side of the door. "Relax, Rodney, the cavalry's here." He waited until the tapping stopped, then pounded on the door with his fist. "We're in here!"

Rodney's head popped up from behind the console. "They found us?"

John just smiled as once more emphatic tapping could be heard from the other side of the door. He clicked his radio. "This is Sheppard, does anyone read me?" His smile faded as he was met with static.

Rodney walked around the counter, absently tapping the screwdriver in one hand on the palm of his other hand. "There must be some sort of dampening field preventing communication in here."

"Why?" Sheppard's brows knitted in confusion.

McKay sighed. "Wish I knew."

Both men's heads turned back to the door as it groaned and opened about three inches.

Rodney peered through the door and abruptly pulled back as a bright light assaulted his eyes. "Turn that damn thing off! What are you trying to do? Blind me?"

"Still your charming self, I see, Rodney." The bright light was replaced with the face of Dr. Zalenka. "You're welcome for opening the door."

"Well you don't have it opened yet, "McKay retorted, rubbing his eyes vigorously.

"Sir?" Ford peered through the narrow opening. "You okay in there?"

"We're fine, Lieutenant, " Sheppard responded, his expression amused at Rodney's antics. "But we'd be better if we could get out of here."

"Yes sir," Ford responded as he glanced to his left. "Dr. Zalenka is working on that right now."

Sheppard nodded. "Glad you found us."

"Yes sir, me too." Ford smiled. "When Dr. Weir couldn't reach you, she sent out teams to search. Good thing we knew you were somewhere in the west pier. We spotted the opened control casing outside this door and figured this was were you were."

"Ah!" Dr. Zalenka's voice drifted through the crack. "This should do it."

Sheppard jumped back as the door slammed shut again.

"Yeah, that was helpful," McKay muttered.

"Stow it, Rodney, at least they know we're in here." Sheppard absently scratched the back of his neck.

"Look, Major," Rodney continued tapping the screwdriver on his hand, his expression uncomfortable. "No one really knows…I mean I haven't told anyone…"

Sheppard smiled. "Relax, Rodney. What's said in the weird Ancient laboratory stays in the weird Ancient laboratory."

McKay stopped fidgeting and smiled briefly at Sheppard. "Right. Thanks. Uhh…same here."

They both looked back at the doorway as the door once more opened slightly, then groaned and sprang open all the way.

"Coming through," Rodney grabbed his pack and trotted past the Major and out the door.

Sheppard shook his head and followed. As he stepped into the corridor, he tapped his radio call button. "Control, this is Sheppard. We're out, thanks to Dr. Zalenka."

"Good to hear you, Major," Weir responded, her voice tinged with relief. "You had us worried."

John smiled. "Nothing McKay and Zalenka couldn't handle. We'll fill you in on the details when we get back."

"Copy that, Major."

Sheppard looked over at Zalenka. "Thanks, Doc."

The Czech doctor smiled back. "You're welcome, Major."

"Took you long enough," Rodney griped as he headed down the hallway towards the command tower.

"We should've let the Major out, and left you in there, McKay," Zalenka retorted as he walked along behind Rodney.

"Yeah fine, whatever." McKay's voice was decidedly annoyed.

Sheppard smiled as he and Ford followed behind the two doctors.

"So, what was it like?" Ford asked quietly.

John glanced at the Lieutenant. "What was what like?"

Ford shrugged. "Being stuck in that room alone with McKay all that time, sir."

Sheppard smiled, his thoughts reflective on what he'd learned about McKay.

"Sir?" Ford questioned.

John arched his eyebrows and smiled. "Interesting, Ford. Very interesting."

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_**Author's notes:** My thanks to Erinmore, Mgosche, and Prmess for their encouragement and honest opinions on this story. Thanks for all the reassurance that my McKay actually sounded like McKay! ((hugs!))_

_I don't own the characters or concepts of Stargate Atlantis (Good grief, I wish I did!) I just borrow them for non-profit fun. :)_

_SGAFan_


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